<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/11181?offset=1380 https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl Tue, 26 Dec 2017 18:06:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl <![CDATA[Building Web UIs With Mojolicious Perl]]> Mojolicious is one of 3 leading web frameworks available in the perl ecosystem (along with Dancer and Catalyst) and by far my favorite.

Mojolicious aims to provide a complete web development experience. It thus has no hard dependencies, comes with a built-in development and production server and many other features one needs to build a web application. It's easy to install, has an applciation generator script and many plugins and extensions.

Libraries for developing Web applications

Address of the bookmark: https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/

]]> Jit https://bioinformaticsonline.com/pages/view/36185/installing-bioscf-perl-module Mon, 09 Apr 2018 04:04:29 -0500 https://bioinformaticsonline.com/pages/view/36185/installing-bioscf-perl-module <![CDATA[Installing Bio::SCF perl module]]> Most Perl modules are written in Perl, some use XS (they are written in C) so require a C compiler (it's easy to get this setup - don't panic), see your OS of choice below to find out how to get the right compiler. Modules may have dependencies on other modules (almost always on CPAN) and cannot be installed without them (or without a specific version of them). Many modules on CPAN require a somewhat recent version of Perl (version 5.8 or above).

More about the basic perl module installation steps check this http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

installing Bio::SCF perl module is daunting task, specieally because of it dependencies. Here is the steps, you need to follow to sucessfully install Bio::SCF module

#sudo apt-get install libbio-scf-perl #trev for visualization of scf file

1. You will need the zlib library which can be found at http://www.zlib.net/.

install zlib library first:

jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] ./configure []
Checking for gcc...
Checking for shared library support...
Building shared library libz.so.1.2.11 with gcc.
Checking for size_t... Yes.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] make []
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc
rm -f libz.so libz.so.1
ln -s libz.so.1.2.11 libz.so
ln -s libz.so.1.2.11 libz.so.1
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.11
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.11
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a
jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] sudo make install []
[sudo] password for jitendra:
rm -f /usr/local/lib/libz.a
cp libz.a /usr/local/lib
chmod 644 /usr/local/lib/libz.a
cp libz.so.1.2.11 /usr/local/lib
chmod 755 /usr/local/lib/libz.so.1.2.11
rm -f /usr/local/share/man/man3/zlib.3
cp zlib.3 /usr/local/share/man/man3
chmod 644 /usr/local/share/man/man3/zlib.3
rm -f /usr/local/lib/pkgconfig/zlib.pc
cp zlib.pc /usr/local/lib/pkgconfig
chmod 644 /usr/local/lib/pkgconfig/zlib.pc
rm -f /usr/local/include/zlib.h /usr/local/include/zconf.h
cp zlib.h zconf.h /usr/local/include
chmod 644 /usr/local/include/zlib.h /usr/local/include/zconf.h
 


2. Now make io_lib-1.9

In order to install this perl extension you have to install io-lib version 1.9 or higher from the Staden library (staden.sourceforge.net). This can be downloaded from https://sourceforge.net/project/showfiles.php?group_id=100316&package_id=108243&release_id=340318 confirm that the package installed correctly look for a library named "libread".

jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] export CFLAGS="-fPIC" && ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for main in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for unistd.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking whether byte ordering is bigendian... no
checking for short... yes
checking size of short... 2
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 8
checking for inline... inline
checking for mode_t... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for cos in -lm... yes
checking for strdup... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating read/Makefile
config.status: creating progs/Makefile
config.status: creating config.h
config.status: executing depfiles commands
jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] make []
make all-recursive
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
Making all in read
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT Read.o -MD -MP -MF ".deps/Read.Tpo" -c -o Read.o Read.c; \
then mv -f ".deps/Read.Tpo" ".deps/Read.Po"; else rm -f ".deps/Read.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_extras.o -MD -MP -MF ".deps/scf_extras.Tpo" -c -o scf_extras.o scf_extras.c; \
then mv -f ".deps/scf_extras.Tpo" ".deps/scf_extras.Po"; else rm -f ".deps/scf_extras.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT translate.o -MD -MP -MF ".deps/translate.Tpo" -c -o translate.o translate.c; \
then mv -f ".deps/translate.Tpo" ".deps/translate.Po"; else rm -f ".deps/translate.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compression.o -MD -MP -MF ".deps/compression.Tpo" -c -o compression.o `test -f '../ztr/compression.c' || echo './'`../ztr/compression.c; \
then mv -f ".deps/compression.Tpo" ".deps/compression.Po"; else rm -f ".deps/compression.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr.o -MD -MP -MF ".deps/ztr.Tpo" -c -o ztr.o `test -f '../ztr/ztr.c' || echo './'`../ztr/ztr.c; \
then mv -f ".deps/ztr.Tpo" ".deps/ztr.Po"; else rm -f ".deps/ztr.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr_translate.o -MD -MP -MF ".deps/ztr_translate.Tpo" -c -o ztr_translate.o `test -f '../ztr/ztr_translate.c' || echo './'`../ztr/ztr_translate.c; \
then mv -f ".deps/ztr_translate.Tpo" ".deps/ztr_translate.Po"; else rm -f ".deps/ztr_translate.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT fpoint.o -MD -MP -MF ".deps/fpoint.Tpo" -c -o fpoint.o `test -f '../abi/fpoint.c' || echo './'`../abi/fpoint.c; \
then mv -f ".deps/fpoint.Tpo" ".deps/fpoint.Po"; else rm -f ".deps/fpoint.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOABI.o -MD -MP -MF ".deps/seqIOABI.Tpo" -c -o seqIOABI.o `test -f '../abi/seqIOABI.c' || echo './'`../abi/seqIOABI.c; \
then mv -f ".deps/seqIOABI.Tpo" ".deps/seqIOABI.Po"; else rm -f ".deps/seqIOABI.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOALF.o -MD -MP -MF ".deps/seqIOALF.Tpo" -c -o seqIOALF.o `test -f '../alf/seqIOALF.c' || echo './'`../alf/seqIOALF.c; \
then mv -f ".deps/seqIOALF.Tpo" ".deps/seqIOALF.Po"; else rm -f ".deps/seqIOALF.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ctfCompress.o -MD -MP -MF ".deps/ctfCompress.Tpo" -c -o ctfCompress.o `test -f '../ctf/ctfCompress.c' || echo './'`../ctf/ctfCompress.c; \
then mv -f ".deps/ctfCompress.Tpo" ".deps/ctfCompress.Po"; else rm -f ".deps/ctfCompress.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOCTF.o -MD -MP -MF ".deps/seqIOCTF.Tpo" -c -o seqIOCTF.o `test -f '../ctf/seqIOCTF.c' || echo './'`../ctf/seqIOCTF.c; \
then mv -f ".deps/seqIOCTF.Tpo" ".deps/seqIOCTF.Po"; else rm -f ".deps/seqIOCTF.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT expFileIO.o -MD -MP -MF ".deps/expFileIO.Tpo" -c -o expFileIO.o `test -f '../exp_file/expFileIO.c' || echo './'`../exp_file/expFileIO.c; \
then mv -f ".deps/expFileIO.Tpo" ".deps/expFileIO.Po"; else rm -f ".deps/expFileIO.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOPlain.o -MD -MP -MF ".deps/seqIOPlain.Tpo" -c -o seqIOPlain.o `test -f '../plain/seqIOPlain.c' || echo './'`../plain/seqIOPlain.c; \
then mv -f ".deps/seqIOPlain.Tpo" ".deps/seqIOPlain.Po"; else rm -f ".deps/seqIOPlain.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT misc_scf.o -MD -MP -MF ".deps/misc_scf.Tpo" -c -o misc_scf.o `test -f '../scf/misc_scf.c' || echo './'`../scf/misc_scf.c; \
then mv -f ".deps/misc_scf.Tpo" ".deps/misc_scf.Po"; else rm -f ".deps/misc_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_scf.o -MD -MP -MF ".deps/read_scf.Tpo" -c -o read_scf.o `test -f '../scf/read_scf.c' || echo './'`../scf/read_scf.c; \
then mv -f ".deps/read_scf.Tpo" ".deps/read_scf.Po"; else rm -f ".deps/read_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT write_scf.o -MD -MP -MF ".deps/write_scf.Tpo" -c -o write_scf.o `test -f '../scf/write_scf.c' || echo './'`../scf/write_scf.c; \
then mv -f ".deps/write_scf.Tpo" ".deps/write_scf.Po"; else rm -f ".deps/write_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT array.o -MD -MP -MF ".deps/array.Tpo" -c -o array.o `test -f '../utils/array.c' || echo './'`../utils/array.c; \
then mv -f ".deps/array.Tpo" ".deps/array.Po"; else rm -f ".deps/array.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compress.o -MD -MP -MF ".deps/compress.Tpo" -c -o compress.o `test -f '../utils/compress.c' || echo './'`../utils/compress.c; \
then mv -f ".deps/compress.Tpo" ".deps/compress.Po"; else rm -f ".deps/compress.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT error.o -MD -MP -MF ".deps/error.Tpo" -c -o error.o `test -f '../utils/error.c' || echo './'`../utils/error.c; \
then mv -f ".deps/error.Tpo" ".deps/error.Po"; else rm -f ".deps/error.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT files.o -MD -MP -MF ".deps/files.Tpo" -c -o files.o `test -f '../utils/files.c' || echo './'`../utils/files.c; \
then mv -f ".deps/files.Tpo" ".deps/files.Po"; else rm -f ".deps/files.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT find.o -MD -MP -MF ".deps/find.Tpo" -c -o find.o `test -f '../utils/find.c' || echo './'`../utils/find.c; \
then mv -f ".deps/find.Tpo" ".deps/find.Po"; else rm -f ".deps/find.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mach-io.o -MD -MP -MF ".deps/mach-io.Tpo" -c -o mach-io.o `test -f '../utils/mach-io.c' || echo './'`../utils/mach-io.c; \
then mv -f ".deps/mach-io.Tpo" ".deps/mach-io.Po"; else rm -f ".deps/mach-io.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT open_trace_file.o -MD -MP -MF ".deps/open_trace_file.Tpo" -c -o open_trace_file.o `test -f '../utils/open_trace_file.c' || echo './'`../utils/open_trace_file.c; \
then mv -f ".deps/open_trace_file.Tpo" ".deps/open_trace_file.Po"; else rm -f ".deps/open_trace_file.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_alloc.o -MD -MP -MF ".deps/read_alloc.Tpo" -c -o read_alloc.o `test -f '../utils/read_alloc.c' || echo './'`../utils/read_alloc.c; \
then mv -f ".deps/read_alloc.Tpo" ".deps/read_alloc.Po"; else rm -f ".deps/read_alloc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT strings.o -MD -MP -MF ".deps/strings.Tpo" -c -o strings.o `test -f '../utils/strings.c' || echo './'`../utils/strings.c; \
then mv -f ".deps/strings.Tpo" ".deps/strings.Po"; else rm -f ".deps/strings.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT traceType.o -MD -MP -MF ".deps/traceType.Tpo" -c -o traceType.o `test -f '../utils/traceType.c' || echo './'`../utils/traceType.c; \
then mv -f ".deps/traceType.Tpo" ".deps/traceType.Po"; else rm -f ".deps/traceType.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT xalloc.o -MD -MP -MF ".deps/xalloc.Tpo" -c -o xalloc.o `test -f '../utils/xalloc.c' || echo './'`../utils/xalloc.c; \
then mv -f ".deps/xalloc.Tpo" ".deps/xalloc.Po"; else rm -f ".deps/xalloc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT vlen.o -MD -MP -MF ".deps/vlen.Tpo" -c -o vlen.o `test -f '../utils/vlen.c' || echo './'`../utils/vlen.c; \
then mv -f ".deps/vlen.Tpo" ".deps/vlen.Po"; else rm -f ".deps/vlen.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_table.o -MD -MP -MF ".deps/hash_table.Tpo" -c -o hash_table.o `test -f '../utils/hash_table.c' || echo './'`../utils/hash_table.c; \
then mv -f ".deps/hash_table.Tpo" ".deps/hash_table.Po"; else rm -f ".deps/hash_table.Tpo"; exit 1; fi
../utils/hash_table.c: In function ‘HashFileOpen’:
../utils/hash_table.c:920:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
sprintf(aname, "%.*s%s", cp-fname+1, fname, hf->archive);
^
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mFILE.o -MD -MP -MF ".deps/mFILE.Tpo" -c -o mFILE.o `test -f '../utils/mFILE.c' || echo './'`../utils/mFILE.c; \
then mv -f ".deps/mFILE.Tpo" ".deps/mFILE.Po"; else rm -f ".deps/mFILE.Tpo"; exit 1; fi
rm -f libread.a
ar cru libread.a Read.o scf_extras.o translate.o compression.o ztr.o ztr_translate.o fpoint.o seqIOABI.o seqIOALF.o ctfCompress.o seqIOCTF.o expFileIO.o seqIOPlain.o misc_scf.o read_scf.o write_scf.o array.o compress.o error.o files.o find.o mach-io.o open_trace_file.o read_alloc.o strings.o traceType.o xalloc.o vlen.o hash_table.o mFILE.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libread.a
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
Making all in progs
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT convert_trace.o -MD -MP -MF ".deps/convert_trace.Tpo" -c -o convert_trace.o convert_trace.c; \
then mv -f ".deps/convert_trace.Tpo" ".deps/convert_trace.Po"; else rm -f ".deps/convert_trace.Tpo"; exit 1; fi
gcc -fPIC -o convert_trace convert_trace.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT makeSCF.o -MD -MP -MF ".deps/makeSCF.Tpo" -c -o makeSCF.o makeSCF.c; \
then mv -f ".deps/makeSCF.Tpo" ".deps/makeSCF.Po"; else rm -f ".deps/makeSCF.Tpo"; exit 1; fi
gcc -fPIC -o makeSCF makeSCF.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT extract_seq.o -MD -MP -MF ".deps/extract_seq.Tpo" -c -o extract_seq.o extract_seq.c; \
then mv -f ".deps/extract_seq.Tpo" ".deps/extract_seq.Po"; else rm -f ".deps/extract_seq.Tpo"; exit 1; fi
gcc -fPIC -o extract_seq extract_seq.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT index_tar.o -MD -MP -MF ".deps/index_tar.Tpo" -c -o index_tar.o index_tar.c; \
then mv -f ".deps/index_tar.Tpo" ".deps/index_tar.Po"; else rm -f ".deps/index_tar.Tpo"; exit 1; fi
gcc -fPIC -o index_tar index_tar.o
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_dump.o -MD -MP -MF ".deps/scf_dump.Tpo" -c -o scf_dump.o scf_dump.c; \
then mv -f ".deps/scf_dump.Tpo" ".deps/scf_dump.Po"; else rm -f ".deps/scf_dump.Tpo"; exit 1; fi
gcc -fPIC -o scf_dump scf_dump.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_info.o -MD -MP -MF ".deps/scf_info.Tpo" -c -o scf_info.o scf_info.c; \
then mv -f ".deps/scf_info.Tpo" ".deps/scf_info.Po"; else rm -f ".deps/scf_info.Tpo"; exit 1; fi
gcc -fPIC -o scf_info scf_info.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_update.o -MD -MP -MF ".deps/scf_update.Tpo" -c -o scf_update.o scf_update.c; \
then mv -f ".deps/scf_update.Tpo" ".deps/scf_update.Po"; else rm -f ".deps/scf_update.Tpo"; exit 1; fi
gcc -fPIC -o scf_update scf_update.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT get_comment.o -MD -MP -MF ".deps/get_comment.Tpo" -c -o get_comment.o get_comment.c; \
then mv -f ".deps/get_comment.Tpo" ".deps/get_comment.Po"; else rm -f ".deps/get_comment.Tpo"; exit 1; fi
gcc -fPIC -o get_comment get_comment.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_tar.o -MD -MP -MF ".deps/hash_tar.Tpo" -c -o hash_tar.o hash_tar.c; \
then mv -f ".deps/hash_tar.Tpo" ".deps/hash_tar.Po"; else rm -f ".deps/hash_tar.Tpo"; exit 1; fi
gcc -fPIC -o hash_tar hash_tar.o ../read/libread.a -lz -lm
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_extract.o -MD -MP -MF ".deps/hash_extract.Tpo" -c -o hash_extract.o hash_extract.c; \
then mv -f ".deps/hash_extract.Tpo" ".deps/hash_extract.Po"; else rm -f ".deps/hash_extract.Tpo"; exit 1; fi
gcc -fPIC -o hash_extract hash_extract.o ../read/libread.a -lz -lm
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT trace_dump.o -MD -MP -MF ".deps/trace_dump.Tpo" -c -o trace_dump.o trace_dump.c; \
then mv -f ".deps/trace_dump.Tpo" ".deps/trace_dump.Po"; else rm -f ".deps/trace_dump.Tpo"; exit 1; fi
gcc -fPIC -o trace_dump trace_dump.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] sudo make install []
[sudo] password for jitendra:
Making install in read
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
test -z "/usr/local/lib" || mkdir -p -- "/usr/local/lib"
/usr/bin/install -c -m 644 'libread.a' '/usr/local/lib/libread.a'
ranlib '/usr/local/lib/libread.a'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
Making install in progs
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
test -z "/usr/local/bin" || mkdir -p -- "/usr/local/bin"
/usr/bin/install -c 'convert_trace' '/usr/local/bin/convert_trace'
/usr/bin/install -c 'makeSCF' '/usr/local/bin/makeSCF'
/usr/bin/install -c 'extract_seq' '/usr/local/bin/extract_seq'
/usr/bin/install -c 'index_tar' '/usr/local/bin/index_tar'
/usr/bin/install -c 'scf_dump' '/usr/local/bin/scf_dump'
/usr/bin/install -c 'scf_info' '/usr/local/bin/scf_info'
/usr/bin/install -c 'scf_update' '/usr/local/bin/scf_update'
/usr/bin/install -c 'get_comment' '/usr/local/bin/get_comment'
/usr/bin/install -c 'hash_tar' '/usr/local/bin/hash_tar'
/usr/bin/install -c 'hash_extract' '/usr/local/bin/hash_extract'
/usr/bin/install -c 'trace_dump' '/usr/local/bin/trace_dump'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Nothing to be done for 'install-exec-am'.
test -z "/usr/local/man/man3" || mkdir -p -- "/usr/local/man/man3"
/usr/bin/install -c -m 644 './man/man3/exp2read.3' '/usr/local/man/man3/exp2read.3'
/usr/bin/install -c -m 644 './man/man3/ExperimentFile.3' '/usr/local/man/man3/ExperimentFile.3'
/usr/bin/install -c -m 644 './man/man3/fread_reading.3' '/usr/local/man/man3/fread_reading.3'
/usr/bin/install -c -m 644 './man/man3/fread_scf.3' '/usr/local/man/man3/fread_scf.3'
/usr/bin/install -c -m 644 './man/man3/fwrite_reading.3' '/usr/local/man/man3/fwrite_reading.3'
/usr/bin/install -c -m 644 './man/man3/fwrite_scf.3' '/usr/local/man/man3/fwrite_scf.3'
/usr/bin/install -c -m 644 './man/man3/read2exp.3' '/usr/local/man/man3/read2exp.3'
/usr/bin/install -c -m 644 './man/man3/read2scf.3' '/usr/local/man/man3/read2scf.3'
/usr/bin/install -c -m 644 './man/man3/read_allocate.3' '/usr/local/man/man3/read_allocate.3'
/usr/bin/install -c -m 644 './man/man3/read_deallocate.3' '/usr/local/man/man3/read_deallocate.3'
/usr/bin/install -c -m 644 './man/man3/read_reading.3' '/usr/local/man/man3/read_reading.3'
/usr/bin/install -c -m 644 './man/man3/read_scf.3' '/usr/local/man/man3/read_scf.3'
/usr/bin/install -c -m 644 './man/man3/read_scf_header.3' '/usr/local/man/man3/read_scf_header.3'
/usr/bin/install -c -m 644 './man/man3/scf2read.3' '/usr/local/man/man3/scf2read.3'
/usr/bin/install -c -m 644 './man/man3/write_reading.3' '/usr/local/man/man3/write_reading.3'
/usr/bin/install -c -m 644 './man/man3/write_scf.3' '/usr/local/man/man3/write_scf.3'
/usr/bin/install -c -m 644 './man/man3/write_scf_header.3' '/usr/local/man/man3/write_scf_header.3'
test -z "/usr/local/man/man4" || mkdir -p -- "/usr/local/man/man4"
/usr/bin/install -c -m 644 './man/man4/Read.4' '/usr/local/man/man4/Read.4'
test -z "/usr/local/include/io_lib" || mkdir -p -- "/usr/local/include/io_lib"
/usr/bin/install -c -m 644 'read/Read.h' '/usr/local/include/io_lib/Read.h'
/usr/bin/install -c -m 644 'read/scf_extras.h' '/usr/local/include/io_lib/scf_extras.h'
/usr/bin/install -c -m 644 'read/translate.h' '/usr/local/include/io_lib/translate.h'
/usr/bin/install -c -m 644 'abi/abi.h' '/usr/local/include/io_lib/abi.h'
/usr/bin/install -c -m 644 'abi/fpoint.h' '/usr/local/include/io_lib/fpoint.h'
/usr/bin/install -c -m 644 'abi/seqIOABI.h' '/usr/local/include/io_lib/seqIOABI.h'
/usr/bin/install -c -m 644 'alf/alf.h' '/usr/local/include/io_lib/alf.h'
/usr/bin/install -c -m 644 'ctf/seqIOCTF.h' '/usr/local/include/io_lib/seqIOCTF.h'
/usr/bin/install -c -m 644 'exp_file/expFileIO.h' '/usr/local/include/io_lib/expFileIO.h'
/usr/bin/install -c -m 644 'plain/plain.h' '/usr/local/include/io_lib/plain.h'
/usr/bin/install -c -m 644 'scf/scf.h' '/usr/local/include/io_lib/scf.h'
/usr/bin/install -c -m 644 'utils/array.h' '/usr/local/include/io_lib/array.h'
/usr/bin/install -c -m 644 'utils/compress.h' '/usr/local/include/io_lib/compress.h'
/usr/bin/install -c -m 644 'utils/error.h' '/usr/local/include/io_lib/error.h'
/usr/bin/install -c -m 644 'utils/mach-io.h' '/usr/local/include/io_lib/mach-io.h'
/usr/bin/install -c -m 644 'utils/misc.h' '/usr/local/include/io_lib/misc.h'
/usr/bin/install -c -m 644 'utils/open_trace_file.h' '/usr/local/include/io_lib/open_trace_file.h'
/usr/bin/install -c -m 644 'utils/tar_format.h' '/usr/local/include/io_lib/tar_format.h'
/usr/bin/install -c -m 644 'utils/traceType.h' '/usr/local/include/io_lib/traceType.h'
/usr/bin/install -c -m 644 'utils/xalloc.h' '/usr/local/include/io_lib/xalloc.h'
/usr/bin/install -c -m 644 'utils/mFILE.h' '/usr/local/include/io_lib/mFILE.h'
/usr/bin/install -c -m 644 'utils/stdio_hack.h' '/usr/local/include/io_lib/stdio_hack.h'
/usr/bin/install -c -m 644 'utils/vlen.h' '/usr/local/include/io_lib/vlen.h'
/usr/bin/install -c -m 644 'utils/hash_table.h' '/usr/local/include/io_lib/hash_table.h'
/usr/bin/install -c -m 644 'utils/os.h' '/usr/local/include/io_lib/os.h'
/usr/bin/install -c -m 644 'ztr/compression.h' '/usr/local/include/io_lib/compression.h'
/usr/bin/install -c -m 644 'ztr/ztr.h' '/usr/local/include/io_lib/ztr.h'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

3. Now install Bio::SCF

Now follows these steps:

tar zxf Bio::SCF.tar
cd Bio::SCF
perl Makefile.PL
make
make test
make install

jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] perl Makefile.PL []
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::SCF
Writing MYMETA.yml and MYMETA.json
jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] make []
cp SCF.pm blib/lib/Bio/SCF.pm
cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm
Running Mkbootstrap for Bio::SCF ()
chmod 644 "SCF.bs"
"/usr/bin/perl" "/usr/share/perl/5.22/ExtUtils/xsubpp" -typemap "/usr/share/perl/5.22/ExtUtils/typemap" SCF.xs > SCF.xsc && mv SCF.xsc SCF.c
Please specify prototyping behavior for SCF.xs (see perlxs manual)
x86_64-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE" -DLITTLE_ENDIAN SCF.c
In file included from /usr/lib/x86_64-linux-gnu/perl/5.22/CORE/perl.h:5546:0,
from SCF.xs:5:
SCF.xs: In function ‘XS_Bio__SCF_get_scf_pointer’:
SCF.xs:57:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ret_val = newSViv((int)scf_data);
^
/usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
#define newSViv(a) Perl_newSViv(aTHX_ a)
^
SCF.xs: In function ‘XS_Bio__SCF_get_scf_fpointer’:
SCF.xs:80:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ret_val = newSViv((int)scf_data);
^
/usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
#define newSViv(a) Perl_newSViv(aTHX_ a)
^
SCF.xs: In function ‘XS_Bio__SCF_scf_free’:
SCF.xs:89:17: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
scf_deallocate((Scf *)scf_pointer);
^
SCF.xs: In function ‘XS_Bio__SCF_get_comments’:
SCF.xs:95:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_comments’:
SCF.xs:108:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_scf_write’:
SCF.xs:121:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_scf_fwrite’:
SCF.xs:137:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_get_from_header’:
SCF.xs:159:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_get_at’:
SCF.xs:186:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_base_at’:
SCF.xs:242:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_at’:
SCF.xs:255:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
rm -f blib/arch/auto/Bio/SCF/SCF.so
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \
-lread -lz \

/usr/local/lib/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
chmod 755 blib/arch/auto/Bio/SCF/SCF.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644
Manifying 1 pod document

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38067/metaplotr-a-perlr-pipeline-for-plotting-metagenes-of-nucleotide-modifications-and-other-transcriptomic-sites Mon, 05 Nov 2018 08:12:45 -0600 https://bioinformaticsonline.com/bookmarks/view/38067/metaplotr-a-perlr-pipeline-for-plotting-metagenes-of-nucleotide-modifications-and-other-transcriptomic-sites <![CDATA[MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites]]> An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Address of the bookmark: https://github.com/olarerin/metaPlotR

]]> Neel https://bioinformaticsonline.com/blog/view/42921/run-bash-script-in-perl-program Sat, 27 Feb 2021 01:42:23 -0600 https://bioinformaticsonline.com/blog/view/42921/run-bash-script-in-perl-program <![CDATA[Run bash script in Perl program !]]> BioPerl is a compilation of Perl modules that can be used to build bioinformatics-related Perl scripts. It is used, for example, in the development of source codes, standalone software/tools, and algorithms in bioinformatics programmes. Different modules are easy to instal and include, making it easier to perform different functions. Despite the fact that Python is commonly favoured over Perl, some bioinformatics software, such as the standalone version of 'alienomics', is written in Perl. Often it's a major problem for beginners to execute certain Unix/shell commands in Perl script, so it's hard to determine which feature is unique to a situation.

Perl provides various features and operators for the execution of external commands (described as follows), which are unique in their own way.
 
They vary slightly from one another, making it difficult for Perl beginners to choose between them.
 
1. IPC::Open2

More at https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module

2. exec””

 syntax: exec "command";

It's a Perl function (perlfunc) that executes a command but never returns, similar to a function's return statement.
While running the command, it keeps processing the script and does not wait until it finishes first, returns false when the command is not found, but never returns true.

3. Backticks “ or qx//

syntax: `command`;

syntax: qx/command/;

It's a Perl operator (perlop) that executes a command and then resumes the Perl script once the command has ended, but the return value is the command's STDOUT.

4. IPC::Open3

syntax: $output = open3(\*CHLD_IN, \*CHLD_OUT, \*CHLD_ERR, 'command arg1 arg2', 'optarg',...);

It is very similar to IPC::Open2 with the capability to capture all three file handles of the process, i.e., STDIN, STDOUT, and STDERR. It can also be used with or without the shell. You can read about it more in the documentation: IPC::Open3.

$output = open3(my $o ut, my $in, 'command arg1 arg2');

OR without using the shell

$output = open3(my $out, my $in, 'command', 'arg1', 'arg2');

5.a2p

syntax: a2p [options] [awkscript]

There is a Perl utility known as a2p which translates awk command to Perl. It takes awk script as input and generates a comparable Perl script as the output. Suppose, you want to execute the following awk statement

awk '{$1 = ""; $2 = ""; print}' f1.txt

This statement gives error sometimes even after escaping the variables (\$1, \$2) but by using a2p it can be easily converted to Perl script:

For further information, you can read it’s documentation: a2p

More help at https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl

6. system()

syntax: system( "command" );

It is also a Perl function (perlfunc) that executes a command and waits for it to get finished first and then resume the Perl script. The return value is the exit status of the command. It can be called in two ways:

system( "command arg1 arg2" );

OR

system( "command", "arg1", "arg2" );

HELP

Here are some useful Perl cheat sheets that can be used as a quick reference guide.-- https://www.pcwdld.com/perl-cheat-sheet

]]> Neel https://bioinformaticsonline.com/pages/view/33841/awesome-perl-frameworks-libraries-and-software-part-4 Fri, 07 Jul 2017 04:11:54 -0500 https://bioinformaticsonline.com/pages/view/33841/awesome-perl-frameworks-libraries-and-software-part-4 <![CDATA[Awesome perl frameworks, libraries and software - PART 4]]>
  • tjstein/php5-fpm-munin-plugins - A set of Munin plugins for PHP5-FPM
  • perusio/nginx-munin - A set of plugins for monitoring nginx with Munin
  • openresty/lua-resty-memcached - Lua memcached client driver for the ngx_lua based on the cosocket API
  • jayjanssen/myq_gadgets - Various iostat style scripts for MySQL
  • apt-mirror/apt-mirror - Official apt-mirror source.
  • kentaro/cinnamon - a simple deploy tool
  • mdom/dategrep - print lines matching a date range
  • kazuho/jailing - super-easy chroot jail builder/runner for Linux
  • teleshoes/tpacpi-bat - ThinkPad ACPI Battery Util
  • hechtus/squeezebox-googlemusic - Squeezebox (Logitech Media Server) Plugin for Google Play Music
  • hexchat/hexchat-addons - Plugins and scripts made for HexChat
  • berekuk/Ubic - Polymorphic service manager.
  • deryckoe/Wordpress-Syntax-Mode-for-Coda-2 - Wordpress Syntax Mode working on Coda 2.0.2
  • squentin/gmusicbrowser - jukebox for large collections of music
  • autodl-community/autodl-irssi - A community-driven fork of autodl-irssi
  • yoshiki/markdown2impress - markdown2impress is script to convert markdown into presentation using impress.js.
  • pagespeed/cpanel - mod_pagespeed module for CPanel WHM
  • liyanage/xcode-text-macros - Some XCode text macros plus a macro overview HTML page generator
  • erlang/eep - Erlang Enhancement ProposalS
  • Koha-Community/Koha - Koha is a free software integrated library system (ILS). Koha is distributed under the GNU GPL version 3 or later. Note: this is a synced mirror of the official Koha repo.
  • vti/bootylicious - LIghtweight blog engine on Mojo steroids!
  • tokuhirom/Furl - pretty fast http client library for perl5
  • miyagawa/Carmel - CPAN Artifact Repository Manager
  • combinatorylogic/clike - A simple C-like language compiler with an extensible syntax and typed macros support
  • cloudflare/CloudFlare-Tools - Tools which enable you to get the full benefit of using the CloudFlare service.
  • untoldwind/alfred2-layout - Alfred 2 Layout workflow
  • nothingmuch/kiokudb - KiokuDB Core
  • katzgrau/chip - A log file multiplexer and monitor. Tail multiple remote or local log files, set actions, and more. A friend to every developer and system admin. Alpha.
  • SethRobertson/git-what-branch - Discover what branch a commit is on, or how it got to a named branch
  • shabble/irssi-docs - In-depth documentation of the Irssi IRC Client
  • kappa/yadisk-sync - Linux syncronizer for Yandex.Disk
  • dotse/dnscheck - DNSCheck code, DNS delegation quality checker.
  • darold/pgcluu - PostgreSQL Cluster performances monitoring and auditing tool
  • cfengine/design-center - CFEngine community-contributed content
  • bestpractical/sd - A distributed issue tracker; upstream is now http://gitorious.org/prophet
  • masak/proto - A a hyper-lightweight dependency tracking and project installation system
  • liblime/LibLime-Koha - LibLime Koha is the most mature of the open source ILS applications. Based on the ground-breaking 3.0 platform (derived from the original Koha offering of 1999), LibLime Koha is a completely web-based open source ILS, with library staff, systems librarians, and library users all accessing LibLime Koha through a web browser. Relying on the MySQL relational database, all LibLime Koha data is readily accessible.
  • ingydotnet/... - Dot Dot Dot
  • gusmaskowitz/apachebuddy.pl - Not written by me, maintained by me : Apachebuddy.pl
  • zaf/asterisk-googletts - Asterisk AGI script that uses Google's translate text to speech service.
  • openresty/lua-resty-core - New FFI-based API for lua-nginx-module
  • openSUSE/kiwi - KIWI OS Image builder
  • FastVPSEestiOu/Antidoto - Linux antimalware and antirootkit tool
  • sorin-ionescu/dotfiles - My command line life.
  • oetiker/smokeping-3.x - reengineered SmokePing, using Extopus as its frontend
  • nekokak/p5-Teng - simple DBI wrapper/ORMapper
  • faiproject/fai - non-interactive system to install, customize and manage Linux systems
  • abh/ntppool - NTP Pool Project
  • willixix/naglio-plugins - Monitoring Plugins by William Leibzon
  • stealth/troubleshooter - setroubleshootd xSports
  • openresty/lua-resty-string - String utilities and common hash functions for ngx_lua and LuaJIT
  • mdxp/cookbooks - My custom Cookbooks for Chef
  • ingydotnet/vroom-pm - Vim Based Slideshow Presentations
  • iamcal/Flickr-StatsD - Mirror of code.flickr.com: Flickr-StatsD
  • ernstsson/Arqua - Architectural quality analysis tool for GCC project
  • qiaoxueshi/FLEXLoader - A jailbreak iOS device tweak which can load FLEX dynamiclly
  • punchdrunker/iOSEmoji - information about unicode6 emoji used in iOS5
  • openresty/replace-filter-nginx-module - Streaming regular expression replacement in response bodies
  • djabberd/DJabberd - The main DJabberd source
  • darold/pgFormatter - A PostgreSQL SQL syntax beautifier that can work as a console program or as a CGI. Download from https://sourceforge.net/p/pgformatter/ and demo site at http://sqlformat.darold.net/
  • aspiers/mysqldiff - tool and CPAN suite backend for comparing MySQL database schemas
  • michaeldexter/vmrc - Virtual Machine rc script
  • keydet89/RegRipper2.8 - RegRipper version 2.8
  • kazuho/kaztools - shellscripts and utilities for myself
  • gknops/adHocGenerate - Wireless ad hoc distribution of iOS applications
  • book/Act - A Conference Toolkit (Git conversion of the Subversion repository)
  • turingou/docor - a smart and tiny README maker using default manifest package.json
  • rjbs/Soviet-Minecraft - a gross hack for chatty control of Minecraft
  • osklil/hls-fetch - Download and decrypt videos served by the HTTP Live Streaming (HLS) protocol.
  • alestic/ec2-expire-snapshots - Delete expired EBS snapshots in Amazon EC2. Install on Ubuntu with: sudo add-apt-repository -y ppa:alestic && sudo apt-get update && sudo apt-get install -y ec2-expire-snapshots
  • rpetrich/objc_api_visibility - Private API checker for iOS. Requires class-dump-z to be in the PATH
  • mojombo/gollum-demo - Gollum test repo
  • mikecardwell/gpgit - Encrypt Email using GnuPG and a pipe
  • lxctl/lxctl - vzctl like utilities for lxc
  • justone/dfm - dotfiles manager
  • miyagawa/cpanfile - Yet another way to declare CPAN dependencies
  • imatix/gitdown - Turn github into your publishing platform
  • grayhemp/pgtoolkit - Tools for PostgreSQL maintenance
  • domm/App-TimeTracker - distributed timetracking from the commandline
  • xaicron/mysqlenv - mysql binary manager
  • tagomoris/fluent-agent-lite - Lightweight log delivery agent works w/ fluentd
  • openresty/lua-resty-upstream-healthcheck - Health Checker for Nginx Upstream Servers in Pure Lua
  • niXman/mingw-builds - Scripts for building the dual-target(32 & 64 bit) MinGW-W64 compilers for 32 and 64 bit Windows
  • lvc/abi-compliance-checker - A tool for checking backward API/ABI compatibility of a C/C++ library
  • chilts/cil - DVCS backed issue tracking system
  • TooTallNate/node-cgi - An http/stack/connect layer to invoke and serve CGI executables.
  • CityGenerator/CityGenerator - CityGenerator is a tool for generating a setting for Fantasy Roleplaying games.
  • yoshinorim/mha4mysql-node - Development tree of Master High Availability Manager and tools for MySQL (MHA), Node (MySQL Server) part
  • Netflix-Skunkworks/jenkins-cli - Simple Jenkins Command Line Interface
  • vrtadmin/clamav-faq - ClamAV FAQ
  • ssinyagin/gerty - A universal framework for device management automation. Eventually a replacement for RANCID... and much more
  • quran/quran.com-images - images using fonts from King Fahed Complex / qurancomplex.com
  • matschaffer/profile - My Bash profile
  • jigish/dotfiles - My configs
  • darold/ora2pg - Ora2Pg is a free tool used to migrate an Oracle database to a PostgreSQL compatible schema. It connects your Oracle database, scan it automaticaly and extracts its structure or data, it then generates SQL scripts that you can load into PostgreSQL.
  • castaway/dbix-class-book - DBIx::Class book
  • brucemiller/LaTeXML - LaTeXML is a TeX and LaTeX to XML translator.
  • OpenDDRdotORG/OpenDDR-Resources - OpenDDR resources
  • revmischa/rtsp-server - Lightweight RTSP/RTP streaming media server
  • oetiker/znapzend - zfs backup with remote capabilities and mbuffer integration.
  • cardinal/cardinal - Cardinal - Ruby compiler for Parrot
  • LibreCat/Catmandu - https://metacpan.org/pod/Catmandu
  • rdvn/zabbix-templates - Various Zabbix templates
  • mischat/shareNice - An ethical way of adding social sharing features to your website, without compromising your users' privacy by dropping tracking cookies on them.
  • kayac/isucon3 - ISUCON3
  • coryarcangel/Pizza-Party-0.1.b - Order pizza over the commandline (circa 2004)
  • msparks/irssiscripts - Scripts for the Irssi IRC client
  • mogui/MDWamp - MDWamp is a client side objective-C implementation of the WebSocket subprotocol WAMP.
  • michaeljamesfitzgerald/Introducing-Regular-Expressions - Example code and target text files for the O'Reilly book Introducing Regular Expressions
  • jeffreykegler/Marpa--R2 - Parse any language you can describe in BNF -- Release 2
  • glensc/nagios-plugin-check_raid - Nagios/Icinga plugin to check current server's RAID status
  • futuretap/iTunesFeaturedCheck - Scrapes the App Store and finds out whether an app is featured on either the App Store homepage or in a specific category
  • yepher/RaZBerry - Notes About ZWave and RazBerry
  • tokuhirom/Minilla - Authorizing tool for CPAN modules
  • rgeissert/http-redirector - Debian mirrors HTTP redirector
  • oetiker/rrdtool-2.x - RRDtool 2.x - The Time Series Database
  • mindreframer/nginx-lua-stuff - some libs for NginX-Lua integration
  • crowbar/barclamp-nagios - [UNMAINTAINED] Crowbar Nagios: System Monitoring
  • andk/cpanpm - CPAN.pm
  • moritz/ilbot - IRC logging bot and web frontend
  • meso-cacase/difff - Webベースのテキスト比較ツール difff《ﾃﾞｭﾌﾌ》
  • elliotchance/mbzdb - Port of the MusicBrainz database to run on other RDBMSs with replication (previously named MB_MySQL.)
  • trapd00r/vidir - edit directory in $EDITOR (better than vim . with netrw)
  • evalEmpire/gitpan - Git repositories for all of CPAN
  • pagekite/Colormake - A simple wrapper around make to colorize the output.
  • manuelkasper/AS-Stats - A simple tool to generate per-AS traffic graphs from NetFlow/sFlow records
  • kazeburo/Monoceros - PSGI/Plack server with event driven connection manager, preforking workers
  • justintime/nagios-plugins - Collection of some handy Nagios plugins
  • justingit/dada-mail - Dada Mail is a simple, web-based mailing list manager. It totally rules.
  • grantm/bcvi - Back-channel vi
  • JeremyJones/Apachetop - apachetop is a console-based tool for monitoring the threads and overall performance of a set of Apache web servers.
  • garu/tweetylicious - a Twitter-like microblogging app in just one file
  • doujiang24/lua-resty-kafka - Lua kafka client driver for the ngx_lua based on the cosocket API
  • HikariKnight/rsu-client - A git repository for the RuneScape Linux/Unix Client Project
  • wimpunk/ddclient - Fork of the original ddclient code
  • tokuhirom/tora - Tora! Tora! Tora!
  • stepb/urxvt-tabbedex - Tabbed plugin for rxvt-unicode with many enhancements
  • rafl/moosex-declare - Declarative syntax for Moose
  • pobox/Moonpig - the moonpig billing system
  • fink/fink - The fink package manager
  • theiostream/theos-ref - Theos Docs! (because there never was a chapter 2)
  • robinbowes/flac2mp3 - flac2mp3 is a tool to convert audio files from flac to mp3 format including the copying of tags.
  • rayman813/coda2-mode-wordpress - Wordpress Syntax Mode/Highlight/Autocomplete for Coda 2
  • hackman/linux-sysadmin-course - Linux System Administration 101
  • deepakdaswani/whatsapp_discover - "Whatsapp Discover" is a tool for getting phone numbers of devices using Whatsapp by real time sniffing from an interface (disabled in this first version) or from a list of pcap files, which can be processed in batch
  • calio/form-input-nginx-module - This is a nginx module that reads HTTP POST and PUT request body encoded in "application/x-www-form-urlencoded", and parse the arguments in request body into nginx variables.
  • bloonix/awesant - Awesant is a log shipper for logstash.
  • AndriiGrytsenko/openssh-ldap-publickey - Wrapper for OpenSSH to store public keys inside the OpenLDAP entry.
  • nikyoudale/symbolicatecrash-mac - A version of the symbolicatecrash script that works for Mac app crash logs
  • mhwest13/Memcached-Munin-Plugin - Memcached Munin Plugins
  • knmnyn/ParsCit - An open-source CRF Reference String Parsing Package
  • c9s/App-gh - GitHub Command-line Utility.
  • bradfitz/shipit - Software Release Tool
  • sukria/WebKeePass - Web interface over a KeePass database
  • naturalist/kelp - A web framework light, yet rich in nutrients.
  • kirei/catt - Certification Authority Trust Tracker
  • kazuho/Starlet - a Plack Server, formerly known as Plack::Server::Standalone::Prefork::Server::Starter
  • dolmen/github-keygen - Easy creation of secure SSH configuration for your Github account(s)
  • bigplum/nginx-tcp-lua-module - A TCP server with lua supporting based on nginx
  • baohaojun/ajoke - Abducting Java Onto Emacs, K is silent.
  • apache/spamassassin - Read-only mirror of Apache SpamAssassin. Submit patches to https://bz.apache.org/SpamAssassin/. Do not send pull requests
  • tsee/Games-Lacuna-Client - A client for the Lacuna Expanse
  • sitaramc/gitpod - local caching server for git when the actual server is on the other side of a (possibly slow) WAN link
  • mjdominus/git-util - Miscellaneous git scripts and utilities
  • kevina/wordlist - SCOWL (and friends).
  • franckcuny/jitterbug - Cross Language Continuous Integration for Git
  • fastmail/towncrier - A status dashboard
  • collectiveintel/cif-v1 - the fastest way to consume threat intelligence.
  • anestisb/WeBaCoo - Web Backdoor Cookie Script-Kit
  • Tarrasch/zsh-autoenv - Autoenv for zsh
  • xme/hoover - Wireless Probe Requests Sniffer
  • spencertipping/caterwaul - A Javascript-to-Javascript compiler
  • openresty/lua-redis-parser - Lua module for parsing raw redis responses
  • mpeters/smolder - Web-based Continuous Integration Smoke Server
  • madscientist/msjnc - MadScientist Juniper Network Connect Session Manager
  • kfdm/irssi-growl - Growl notification script for irssi
  • jimsalterjrs/sanoid - Policy-driven snapshot management and replication tools. Currently using ZFS for underlying next-gen storage, with explicit plans to support btrfs when btrfs becomes more reliable. Primarily intended for Linux, but BSD use is supported and reasonably frequently tested.
  • duritong/puppet-nagios - a nagios module for puppet
  • szabgab/screencasts - The translated captions of my screencasts
  • openresty/resty-cli - Fancy command-line utilities for OpenResty
  • kre/Kinetic-Rules-Engine - Source code for KRE
  • helloandre/cr48 - my programs that i've put on cr48
  • csirtgadgets/massive-octo-spice - the fastest way to consume threat intelligence
  • agentzh/sshbatch - SSH::Batch for cluster operations
  • SPORE/api-description - SPORE description for API
  • xilinus/prototypeui - Prototype UI
  • tagomoris/isucon - isucon web applications and tools
  • perl6/doc - Perl 6 documentation (tools and docs)
  • hirose31/redis-traffic-stats - Redis query analyzer for counting, traffic stats by command
  • gjreda/pydata2014nyc - Materials for my pandas tutorial at PyData 2014, NYC
  • genaev/vmd - vkontakte music downloader
  • dalibo/sqlserver2pgsql - Migration tool to convert a Microsoft SQL Server Database into a PostgreSQL database, as automatically as possible
  • symkat/Stalker - Records and correlates nick!user@host information
  • lvc/japi-compliance-checker - A tool for checking backward API/ABI compatibility of a Java library
  • justinabrahms/jlilly-bashy-dotfiles - This is a collection of my dotfiles not related to either vim or emacs. Mostly just bashy stuff.
  • interchange/interchange - Interchange
  • ingydotnet/jemplate - Industrial strength JavaScript template framework
  • depesz/explain.depesz.com - Webpage for showing easier to read version of PostgreSQL explains
  • Webconverger/webc - Webconverger's curated chroot from which updates originate
  • SSLMate/sslmate - The SSLMate Client - Buy and Manage SSL Certs from the Command Line
  • stayradiated/dotfiles - Just my configs for CRUX and OS X
  • openresty/lua-resty-lock - Simple nonblocking lock API for ngx_lua based on shared memory dictionaries
  • nickspacek/Net-Google-Tasks - Interface to Google Tasks
  • jdavis/dotfiles - Config files for various things
  • evadne/LESS.mode - LESS syntax mode for SubEthaEdit and Coda
  • dotse/zonemaster - The Zonemaster Project
  • darold/squidanalyzer - Squid Analyzer parses Squid proxy access log and reports general statistics about hits, bytes, users, networks, top URLs, and top second level domains. Statistic reports are oriented toward user and bandwidth control.
  • vti/showmetheshell - HTML5 WebSocket Shell
  • oalders/http-browserdetect - Determine the Web browser, version, and platform from an HTTP user agent string
  • marksteele/collectd-plugins - Collectd Plugins
  • kristofg/rifec - Receive Images From Eye-Fi Cards
  • kirei/fpdns - Net::DNS::Fingerprint
  • gjospin/PhyloSift - Phylogenetic and taxonomic analysis for genomes and metagenomes
  • chrispix/symbolicatecrash-fix - A patch of Apple's symbolicatecrash script, broken in XCode4
  • billkarwin/bk-tools - Scripts I wrote to help using MySQL and Percona products.
  • adelton/docker-freeipa - FreeIPA server and client in Docker containers; see hub.docker.com for the images:
  • OWASP/O-Saft - O-Saft - OWASP SSL audit for testers
  • yllan/moedict-mac - 轉換教育部國語辭典為 Mac 內建字典
  • tokuhirom/cpan-outdated - detect outdated CPAN modules
  • openwebwork/webwork2 - Course management front end for WeBWorK
  • nicolaspanel/libsvm.net - An easy way to use Support Vector Machines in your .NET projects (c# code)
  • jodrell/unbound-block-hosts - a script to convert Dan Pollock's ad blocking hosts file into Unbound local-data.
  • davepacheco/jsstyle - cstyle-based JavaScript style checker
  • cloudflare/lua-resty-cookie - Lua library for HTTP cookie manipulations for OpenResty/ngx_lua
  • c9s/github-taiwan - Taiwan Developers on Github
  • PadreIDE/Padre - Offical repository of the core Padre code
  • rovo89/XposedTools - These tools can be used to compile and package the Xposed framework.
  • openresty/nginx-devel-utils - Utilities for nginx module development
  • openSUSE/obs-build - OBS build script, can be used with OBS or stand alone
  • nichtich/ditaa-markdown - process ditaa diagrams embedded in pandoc markdown
  • bestpractical/prophet - A disconnected, replicated p2p database -- upstream is now http://gitorious.org/prophet
  • aparks517/convert-websters - Convert Webster's Unabridged Dictionary from Project Gutenberg to OSX dictionary
  • ap/titlecase - An attempt to refactor John Gruber’s Title Case program
  • yko/mojo.vim - Vim syntax for mojo epl templates in Mojo projects
  • tseemann/prokka - Rapid prokaryotic genome annotation
  • peterkeen/calorific - Command-line nutrient tracking tool
  • openresty/lua-resty-dns - DNS resolver for the nginx lua module
  • maxmind/MaxMind-DB - Spec and test data for the MaxMind DB file format
  • kazeburo/Kurado - monitor metrics
  • bigpresh/Dancer-Plugin-Database - Dancer::Plugin::Database - easy database support for Dancer applications
  • BaldMansMojo/check_vmware_esx - chech_vmware_esx Fork of check_vmware_api.pl
  • vanstyn/RapidApp - Turnkey ajaxy webapps
  • taylorchu/baker - The bash static site generator with real template engine
  • sujaikumar/assemblage - Tools for working with second gen assemblies, fasta sequences, etc
  • obfuscurity/nagios-scripts - Custom scripts written for Nagios
  • miyagawa/AnyEvent-Twitter-Stream - AnyEvent based Twitter stream consumer
  • miyagawa/AnyEvent-Redis - Asynchronous Redis client
  • drdrang/tp-planner - A set of scripts for printing TaskPaper documents compactly for inserting into a "Junior" sized planner.
  • ccurtsinger/stabilizer - Stabilizer: Rigorous Performance Evaluation
  • zrlram/afterglow - graph visualization tool
  • utcompling/OpenNLP-Models - A project for code to create models from existing corpora and distribute models.
  • theory/dbix-connector - Fast, safe DBI connection management
  • redondos/mutt - mutt configuration
  • p5-app-adventcalendar/p5-app-adventcalendar - let's make advent calendar!
  • motemen/Teto - nicovideo stream player
  • lifeforms/irssi-smartfilter - Irssi JOIN/QUIT smart filter for busy channels
  • genehack/app-gitgot - A tool to make it easier to manage multiple code repositories using different VCSen
  • ytoolshed/multipkg - Automation for package builds
  • willemk/varnish-mobiletranslate - Tool to translate the latest mobile detect script into varnish
  • sashahilton00/spotify-connect-resources - A repository to hold any data/stuff related to reversing the Spotify Connect protocol. Mostly just data dumps at the moment, but if you have something to add to it, be it an implementation, information or just another data dump, make a PR and I will add it asap.
  • kumina/nagios-plugins-kumina - A collection of Nagios plugins that we package.
  • jbergantine/django-template.mode - Django Template Syntax mode for Panic Coda 2
  • jasta/android-dev-tools - Collection of developer tools for working with Android.
  • devel/PowerDNS-API - HTTP API for the PowerDNS Database
  • daniel-nichter/hackmysql.com - Deprecated tools from HackMySQL.com
  • agentzh/cheater - A tool and a language that help generating random complex database instance based on predefined rules
  • GMOD/GBrowse - the Generic Genome Browser
  • yaoweibin/nginx_limit_access_module - support to deny specific variable with HTTP POST interface
  • yanick/git-cpan-patch - System to write patches against CPAN modules via Git
  • synacorinc/dtk - DTK (data toolkit) is a suite of tools for parsing, analyzing, and graphing logs and other datasets.
  • schweikert/postgrey - Postfix Greylisting Policy-Daemon
  • noodba/myawr - awr of MySQL
  • marcusramberg/Mojolicious-Plugin-OAuth2 - OAuth support for Mojolicious
  • lukeredpath/LRMocky - A port of jMock 2.0 for Objective-C
  • linux-test-project/lcov - LCOV
  • gamelinux/echidna - Network Security Monitoring Framework
  • datameet/india-election-data - To map publicly available datasets related to General Assembly (Lok Sabha) elections in India.
  • cmatsuoka/figlet-fonts - A collection of fonts for FIGlet
  • ambs/Books - My repository to book projects... if I eventually have the guts to write more than one...
  • abw/Template-TT3 - A working prototype of the TT3 template language
  • yasuaki/git-doc-ja - Japanese translation of git/Documentation/
  • xdata-skylark/libskylark - Sketching-based Distributed Matrix Computations for Machine Learning
  • typester/nim - minimal command-line based contents generator
  • trapd00r/utils - Small useful utilities for everyday work
  • plack/Plack-Middleware-Session - A very minimalist session library for Plack
  • openxpki/openxpki - OpenXPKI Code
  • onishi/mysqldiff - mysqldiff - mysql scheme diff
  • mikegrb/App-otfile - Serve a single file, once, via HTTP over the local network.
  • mikebrittain/Wesley - Compress and optimize the JPEG, PNG, and GIF files used in your site’s HTML and CSS.
  • kthakore/frozen-bubble - Making frozen bubble cross platform
  • hluk/vimColorsToQtCreator - Convert vim color schemes so they can be used in Qt Creator.
  • cvicente/Netdot - Network Documentation Tool
  • ciembor/TerminalHero - Linux society's response to Guitar Hero. :)
  • carloslima/dhsnapshot - RSnapshot-like backups to DreamHost Backup Service
  • alecchen/doxygen-lua - Make Doxygen support Lua
  • AgileBits/onepassword-utilities - Utilities for 1Password
  • yrmt/dotfiles - a few of yrmt (beastie)'s dotfiles
  • willixix/WL-NagiosPlugins - Clone of naglio-plugins repository for those using old name
  • rafl/moosex-method-signatures - Method declarations with type constraints and no source filter
  • proftpd/proftpd - ProFTPD source code
  • plainblack/Wing - Next generation web services toolkit.
  • msimerson/NicTool - NicTool: a DNS management solution
  • j0hnnMcCock/fuckNSA - fuckNSA
  • dbsrgits/sql-translator - SQL::Translator (SQLFairy)
  • cryptax/dextools - Miscellaenous DEX (Dalvik Executable) tools
  • cosimo/varnish-accept-language - An experimental VCL extension to squash client Accept-Language headers
  • catap/nginx-catap - catap's nginx repository
  • ConSol/omd - OMD - Open Monitoring Distribution Labs Edition
  • 42Lines/cq5tools - Handy CLI tools for working with Adobe's CQ5 CMS product
  • thomasfrivold/SilentBob - SilentBob Firewall
  • starlilyth/Linux-PoolManager - Web based miner manager for CGMiner and clones (SGMiner, Keccak, etc) on Linux (PIMP/BAMT/SMOS, Debian, RedHat/Centos).
  • perl-pod/pod-simple - Framework for Parsing and Formatting POD
  • openresty/opsboy - A rule-based sysadmin tool that helps setting up complex environment for blank machines
  • nekokak/qudo - job queue system
  • moshen/Image-Term256Color - Display images in your 256 color terminal! (kinda) - superseded by https://github.com/moshen/gotermimg
  • kazuho/cppref - man-style access to cppreference.com documents
  • jquelin/dist-zilla-plugin-git - dist::zilla plugin to update your git repository after release
  • jonlives/nagios-jenkins-plugin - A nagios plugin for which lets you check jenkins jobs according to various criteria.
  • ikebe/Pickles - Tiny Web Application Framework.
  • gws/munin-plugin-couchdb - Munin plugins for graphing CouchDB statistics.
  • dyne/gitzone - git-based zone management tool for static and dynamic domains
  • duggan/shlint - A shell linting utility.
  • bloonix/logstash-delete-index - A script to delete Elasticsearch indices of Logstash
  • angavrilov/df-structures - Dwarf Fortress data structure descriptions
  • alibaba/tengine-website - The source code of Tengine's website (tengine.taobao.org)
  • SpiderLabs/thicknet - TCP session interception and injection framework
  • AssetTracker/rt-extension-assettracker - Asset Tracker is an extension for Request Tracker. It integrates asset tracking with your favorite ticketing system.
  • tokuhirom/Daiku - Yet another build tool on Perl5
  • schweikert/mailgraph - Mail plotting script
  • plainblack/Lacuna-Server-Open - The open source Lacuna Server repository.
  • netoptimizer/IPTV-Analyzer - Fast MPEG2 Transport Stream Analyzer, based on Netfilter kernel module
  • kvorg/mojo-handbook - Mojolicious Handbook: a temporary documentation resource for Mojolicious
  • kablamo/VimDebug - Integrate your debugger with Vim. Currently supports Perl, Python, and Ruby. This code is very much in beta.
  • genome/gms - The Genome Modeling System installer (BETA).
  • franckcuny/presque - a simple redis/tatsumaki message queue
  • dgl/cgiirc - CGI:IRC web based IRC client
  • dann/angelos - yet another web application framework
  • Bibzball/Git-Mediawiki - Gate between git and mediawiki
  • trustly/pci-blackbox - PCI-DSS compliant card system built on PostgreSQL and PL/pgSQL
  • tomill/Template-Semantic - Use pure XHTML/XML as a template
  • raboof/realtimeconfigquickscan - Linux configuration checker for systems to be used for real-time audio
  • postcasio/coda2-modes - Syntax modes for Coda 2.
  • norm/homedir - Public home directory files
  • nindwen/config - Arch Linux config-files
  • lvc/pkgdiff - A tool for visualizing changes in Linux software packages
  • jjn1056/DBIx-Class-Migration - Use DBIC::DeploymentHandler and DBIC::Fixtures together for a sane database versioning workflow
  • hpcugent/easybuild-easyconfigs - A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
  • gfx/p5-Data-Validator - Type constraints based data validator for Perl5
  • evalEmpire/method-signatures - Method and function declarations with signatures, no source filter
  • yogan/cope - A colourful wrapper for terminal programs
  • trinityrnaseq/trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
  • tokuhirom/p5-router-simple - simple http router
  • thiagorondon/OpenData-BR - OpenData-BR
  • skx/slaughter - The Slaughter system-administration & configuration tool.
  • mizzy/webiblo - Web to ebook project
  • miyagawa/Dist-Milla - Opinionated and Unobtrusive distribution builder
  • meermanr/TVSeriesRenamer - Script for renaming files in a digital video collection. Automatically fetches episode titles from the web.
  • markround/Cacti-iostat-templates - A set of templates to monitor iostat statistics on Unix systems
  • gvalkov/gitolite-sshkey-form - A web app for submitting ssh public keys directly to gitolite
  • ftilmann/latexdiff - Compares two latex files and marks up significant differences between them. Releases on www.ctan.org and mirrors
  • eprints/eprints - EPrints Core
  • eksopl/fuuka - Fuuka Imageboard Archiver
  • aelse/dot-ssh-config - Generate SSH client configurations with support for tunnels
  • Perl5-Alien/Alien-Base - Base classes for Alien:: modules
  • Ovid/example-test-training-material - Sample Code From Ovid's Introductory Testing Course
  • LuRsT/vspark - Like spark, but vertical
  • DjebbZ/Drupal-PHPStorm-Live-Templates - PHPSTorm Live Templates (aka code snippets) for Drupal 7
  • zamiron/ru4sphinx - Creating Russian voice model for cmu-sphinx
  • yappo/p5-Data-Model - Data::Model is Data/Object Mapper and Model Manager.
  • xaicron/p5-www-youtube-download - YouTube video download interface.
  • vti/protocol-websocket - Protocol::WebSocket
  • ukigumo/Ukigumo-Server - This is a ukigumo server application.
  • treasonx/environment - Personal Environment Files (vim, bash, etc)
  • sartak/app-nopaste - easy access to any pastebin
  • rolandwalker/emacs-travis - Travis CI recipe for Emacs libraries.
  • msimerson/sentry - Bruteforce attack blocker (ssh, FTP, SMTP, and more)
  • lookout/ngx_borderpatrol - Edge-authentication
  • ipfire/ipfire-2.x - IPFire 2.x development tree
  • dgl/cpangrep - Search code on CPAN with Regexps
  • bugzilla/bugzilla - Read-only mirror of Bugzilla source from git.mozilla.org/bugzilla/bugzilla.git. Tests at https://travis-ci.org/bugzilla/bugzilla –
  • avar/irssi-bitlbee-facebook-rename - A irssi script to rename chat.facebook.com nicks in bitlbee from e.g. "u1359078110" to "AEvarArnfjord"
  • artm/qtcreator-solarized-syntax - Solarized style for Qt Creator's syntax highlighter
  • SharkHunter/Channel - Channel Browse plugin for PMS
  • OpenElectronicsLab/eeg-mouse - The eeg-mouse is a project to attempt to control a mouse with eeg signals.
  • yusukebe/App-revealup - HTTP Server app for viewing Markdown formatted text as slides
  • yappo/JSTAPd - JSTAPd is Ajax application friendly Javascript Unit Test Server.
  • wayfind/polite - 一个为前端开发者量身打造的Vim配置和插件精选集
  • smallfish/lua-resty-beanstalkd - non-blocking beanstalkd client lib for ngx_lua
  • sixteencolors/sixteencolors - Sixteen Colors ANSI/ASCII Art Archive
  • perigrin/moosex-poe - The illicit love child of Moose and POE
  • ole-tange/tangetools - Ole Tanges personal tools
  • nothingmuch/class-mop - Mirror of Class-MOP.git
  • mjollnir/sf2debpkg - Symfony2 Debian Packaging
  • miyagawa/plack-dispatching-samples - Examples of Plack dispatcher using various CPAN modules
  • miyagawa/Webhook-Growler - Receives Web hooks over Reverse HTTP and notifies via Growl
  • miyagawa/HTTPx-Weblet - the Request/Response objects formerly known as the-old-Plack::Request
  • miyagawa/Corona - Coro based high-performance, asynchronous PSGI web server
  • mengwong/org-asana - Roundtrip synchronization and bidirectional replication between Emacs Org-mode and Asana.com.
  • keydet89/Tools - Tools from WFA 4/e, timeline tools, etc.
  • kan/moxy - Mobile web development proxy
  • goccy/p5-Compiler-Tools-CopyPasteDetector - detect Copy and Paste of Perl5 Codes
  • ctcherry/easy_php_dev - Collection of tools to quickly setup a dynamic PHP dev environment on OSX
  • chromatic/CPAN-Dark - Manage your own DarkPAN
  • chansen/p5-http-tiny - Tiny HTTP Client
  • bobtfish/catalystx-simplelogin - Simple login controller and template bundle for Catalyst
  • bestpractical/git-sync - A tool to synchronize multiple git repositories
  • Gilwyad/mailnesia.com - Anonymous Email in Seconds
  • Ensembl/ensembl-rest - Language agnostic RESTful data access to Ensembl data over HTTP
  • CalculatedContent/tsvm - experiments testing transductive svm for my blog posts
  • zby/WebNano - A really minimalistic web framework.
  • wtsi-hgi/docker-proxify - Allows building and running docker container images from behind a corporate proxy
  • tokuhirom/p5-psgiref - (DEPRECATED)just a prototype!
  • robelix/hard-dj - arduino based DJ MIDI cotroller using Harddisks as jog wheels
  • rjbs/dzil.org - the source for dzil.org
  • perldoc-jp/module-pod-jp - 日本語訳したモジュールをおく場所その2
  • motemen/Plack-Middleware-WebSocket - WebSocket handshake helper middleware
  • kivitendo/kivitendo-erp - Web-based ERP system for the German market
  • hinrik/hailo - A conversation bot using Markov chains
  • g0v/moedict-data-csld - 中華語文知識庫 資料檔
  • freenode/gms - Group Management System
  • doy/reply - read, eval, print, loop, yay!
  • digitalbazaar/json-ld - A Context-based JSON Serialization for Linked Data
  • dcantrell/ldap-for-dhcp - OpenLDAP support for dhcpd in ISC dhcp
  • cjfields/biome - An experimental Moose-based BioPerl implementation
  • brennen/git-feed - git-feed: a script to generate Atom feeds for git commit logs
  • bobthecow/PHP-HTML.mode - A fork of Coda 1.x's PHP-HTML syntax mode. Doesn't work with 2.x :(
  • ant0ine/MongoDB-RDF - Stores RDF-JSON documents in MongoDB
  • adrian-bl/bitflu - Bitflu BitTorrent Client
  • MG-RAST/MG-RAST - metagenomic analysis server site code
  • xaicron/pm-uninstall - Uninstall modules
  • windytan/bitocular - A tool to quickly examine the general structure of a file.
  • toreanderson/clatd - A 464XLAT CLAT implementation for Linux
  • sitaramc/map - Simpler than xargs. More power than xargs.
  • silvansky/macscripts - My Mac OS X scripts for different needs (may need some of my Mac OS X command line utils)
  • nekokak/p5-Kamui - Plack base framework
  • nabokov/mecab-dic-overdrive - create new mecab dic file, with score adjustment in accordance with existing terms.
  • miyagawa/Catalyst-Engine-PSGI - PSGI engine for Catalyst
  • melo/scripts - My personal script stash
  • liedekef/spacewalk_scripts - Several spacewalk scripts
  • kraih/mojolicio.us - Mojolicious Website
  • interconnectapp/discuss - A place to discuss interconnect
  • glidenote/dotfiles - my dotfiles
  • elubow/ec2-consistent-snapshot - EC2 Consistent Snapshot with Mongo Support
  • dalibo/pgshark - Messing with PostgreSQL network traffic to make some usefull things
  • clkao/AnyMQ - Simple message queue based on AnyEvent
  • chrisbra/vim_faq - The Vim FAQ from http://vimdoc.sourceforge.net/
  • PerlDancer/advent-calendar - Articles for the advent calendar
  • Kimtaro/jisho.org - The source for classic.jisho.org
  • shoorick/mojowka - Small wiki based on top of Mojolicious::Lite
  • ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/36857/%E2%80%9Cone-code-to-find-them-all%E2%80%9D-a-perl-tool-to-conveniently-parse-repeatmasker-output-files Mon, 04 Jun 2018 03:45:15 -0500 https://bioinformaticsonline.com/bookmarks/view/36857/%E2%80%9Cone-code-to-find-them-all%E2%80%9D-a-perl-tool-to-conveniently-parse-repeatmasker-output-files <![CDATA[“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files]]> Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all

    ]]>     Poonam Mahapatra     https://bioinformaticsonline.com/opportunity/view/25323/project-fellow-positions-at-csir-ihbt-palampur Tue, 01 Dec 2015 05:45:58 -0600 <![CDATA[Project Fellow Positions at CSIR-IHBT Palampur]]> Walk-in-Interview is scheduled to be held on the date as mentioned below for selection of Suitable candidates in the following areas under the different Sponsored/CSIR Networked Projects on purely temporary basis for the duration of the project(s) or till completion of projects whichever is earlier:

    Sponsored/CSIR Networked Project:
    (i) Genomics and Informatics Solutions for Integrating Biology (GENESIS)" [BSC-0121] (up to March, 2017).
    (ii) Profiling and characterization of early phase differential mi-RNA (s) responsible for downstream developmen of insulin resistance in hMSC derived adipocytes. (GAP-0188) [up to 31.03.2018].

    Position: Project Fellow (2 position)
    Age : 28 years as on 18.12.15
    Salary : Rs.12,000/- P.M.
    Rs.14,000/- P.M.
    as per the funds provisions in the respective projects.
    Eligibility Criteria : 1st Class B. Tech. in Bioinformatics/ Computational Biology
    OR
    M.Sc. in Bioinformatics/ Computational Biology with 55% marks
    OR
    M.Tech. in Bioinformatics/ Computational Biology with 55% marks
    OR
    M.Sc. in any field of Life Science with Diploma in Bioinformatics

    Selection Procedure : Walk In Interview

    Date : 18 Dec , 2015
    Time : 10:00 A.M.
    Venue : CSIR-IHBT Palampur (H.P.)

    ]]>         https://bioinformaticsonline.com/opportunity/view/25866/jrf-bioinformatics-at-national-chemical-laboratory Sun, 03 Jan 2016 05:59:05 -0600 <![CDATA[JRF Bioinformatics at National Chemical Laboratory]]> Junior Project Fellow Bioinformatics
    Eligibility : ME/M.Tech, MSc(Bio-Informatics)
    Location : Pune
    Last Date : 08 Jan 2016
    Hiring Process : Written-test, Face to Face Interview
    National Chemical Laboratory

    Junior Project Fellow Jobs opportunity in National Chemical Laboratory on contract basis
    Project Code : BSC0117
    Title of the Project : Plant?Microbe and Soil Interactions (PMSI)
    No. of Post : 01
    Qualification : M.Tech. / M.Sc. in Bioinformatics from a recognized university with minimum of 55% marks (aggregate) and sound Bioinformatics knowledge / experience
    Desirable : Good knowledge of Linux (command line and GUI) and SQL; Java / Perl / Python / R / Bash programing / scripting; Analysis of NGS data; Protein modeling / docking; Development and maintenance of web & database servers, etc
    Emoluments : Rs. 16,000/?
    Age Limit : 28 Years
    Selection Procedure : Written Test / Interview
    How to apply
    Applications neatly typed in the prescribed proforma (enclosed herewith) duly completed and signed together with photo?copies of relevant certificates/ testimonials and photograph should be addressed to : The Head, Biochemical Sciences Division, Attn : Dr. Narendra Kadoo, CSIR?National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411 008, so as to reach on or before 08/01/2016. Please superscribe the envelop “Application for Junior Project Fellow (Project: BSC0117)”.

    More at http://www.ncl-india.org/files/JoinUs/JobVacancies/TemporaryJobs.aspx?

    ]]>         https://bioinformaticsonline.com/researchlabs/view/25993/hoffman-lab Tue, 12 Jan 2016 02:47:41 -0600 <![CDATA[Hoffman Lab]]> They develop machine learning techniques to better understand chromatin biology. These models and algorithms transform high-dimensional functional genomics data into interpretable patterns and lead to new biological insight.

    https://www.pmgenomics.ca/hoffmanlab/

    ]]>         https://bioinformaticsonline.com/bookmarks/view/26356/spines Tue, 09 Feb 2016 05:07:15 -0600 https://bioinformaticsonline.com/bookmarks/view/26356/spines <![CDATA[Spines]]>

    Spines

    Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

    Access Spines here.

    http://www.broadinstitute.org/science/programs/genome-biology/spines

    Address of the bookmark: http://www.broadinstitute.org/science/programs/genome-biology/spines

    ]]>     Jitendra Narayan